Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
MTA1

Cell type

Cell type Class
Digestive tract
Cell type
HCT 116
Primary Tissue
Colon
Tissue Diagnosis
Carcinoma

Attributes by original data submitter

Sample

source_name
Cell line HCT116
cell line
HCT116
tissue
colon
morphology
epithelial
disease
colorectal carcinoma
antibody
MTA1

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Formaldehyde crosslinked cells were lysed on ice by resuspending and repeated pipetting with 10 cell pellet volumes of RIPA buffer( 50 mM Tris 7.4, 150 mM NaCl, 2 mM EDTA, 0.1% SDS, 0.5% NP-40 and 0.5% deoxycholate).The cells lysates was sonicated to generate DNA fragments of 200-500 bp, centrifuged for 10 min at 12,000 g, and the supernatant was directly used for immunoprecipitation. Place the tube containing the Pierce™ ChIP-grade Protein A/G Magnetic Beads on the magnetic ,then, discard the supernatant. Wash the beads for three times with 1ml 0.1M sodium phosphate Buffer . ChIP-seq was performed by using ThruPLEX® DNA-seq kit (R400427; Rubicon Genomics) according to manufacturer’s instructions. The PCR products corresponding to 300-500 bps were gel purified, quantified and stored at -80 oC until used for sequencing. ChIP-Seq sequencing was performed on NextSeq500 platform with 151 bp paired-end sequencing.

Sequencing Platform

instrument_model
NextSeq 500

hg38

Number of total reads
12157937
Reads aligned (%)
62.8
Duplicates removed (%)
1.9
Number of peaks
559 (qval < 1E-05)

hg19

Number of total reads
12157937
Reads aligned (%)
61.5
Duplicates removed (%)
2.4
Number of peaks
275 (qval < 1E-05)

Base call quality data from DBCLS SRA